The genus Microcystis is responsible for many ‘nuisance’ and toxic algal blooms that threaten various fresh water bodies in Australia. Of particular importance is the taxa Microcystis aeruginosa which is highly prevalent and contains a deep pangenome, leading to substantial genomic variability between strains. It has been established that certain cyanobacteria, including hepatotoxic Microcystis species, annually transition between planktonic and benthic forms. Benthic-planktonic coupling has been associated with an increase in the abundance of Microcystis during spring and summer, often resulting in dense surface blooms, followed by the sedimentation of colonies to the benthos during the cooler months. In order to improve industry predictions of the risk, timing and severity of toxic Microcystis blooms, this project aims to investigate the biological mechanisms and environmental triggers that cause bloom development. Through a range of classical isolation techniques and various ‘-omic’ studies this project will study the recruitment of benthic dwelling Microcystis species to surface waters.

PhD Thesis underway by Caitlin Romanis.

This project characterised the acute cytotoxicity of a hydraulic fracturing fluid using a human gastrointestinal cell line and, using this data, contribute to the understanding of potential human health risks posed by Coal Seam Gas (CSG) extraction in Queensland.

Honours Thesis completed by Madeleine Payne in October 2012.

This project established a bioassay using mouse embryonic stem cells to assess the effects of the cyanobacterial toxin, cylindrospermopsin, on early embryonic development. Using embryonic stem cells cultured in vitro as a model for embryos in vivo, the project will analysed cytotoxicity of cylindrospermopsin, its effects on cell morphology, and on gene expression.

Wastewater surveillance for SARS-CoV-2 has proven effective in supporting COVID control efforts globally, allowing detection of novel infection clusters, supporting assessment of community transmission risk, and providing an important reminder to the public to remain vigilant in adhering to social distancing and other public health policies. Surveillance is achieved through the application of highly sensitive molecular diagnostic tools. In such applications, the diagnostic markers employed for wastewater surveillance can be improved, but more genetic information is needed. Whole genome sequencing (WGS) provides the most conclusive and robust approach to providing more genomic material for analysis.

This project addresses a recent priority research call from WaterRA for programs to extend capacity for wastewater testing for SARS-CoV-2. This includes the evaluation and implementation WGS methods for SARS-CoV-2 in wastewater and seek to overcome current limitations in detection sensitivity that have prevented their use in Australia to date.

The protozoan parasites, Cryptosporidium and Giardia represent a major public health concern of water utilities in developed nations. In Australia, marsupials, cattle and sheep are the dominant animals inhabiting water catchment areas and contribute a large volume of manure to catchments. Cryptosporidium fayeri, one of the main species identified in marsupials, was identified in a 29-year-old woman in Sydney in 2009 with identical subtypes found in marsupials in the area. There have also been reports of C. parvum and C. hominis (the most common species found in humans), in kangaroos, a wallaby, possums and bandicoots by independent groups, as well as high prevalence’s of zoonotic genotypes of Giardia in marsupials.

This project conducted a comprehensive study of genotypes of Cryptosporidium and Giardia present in marsupials, pre-weaned cattle and sheep and STP sites, over a three-year period to gain a more thorough understanding of the zoonotic risk these parasites pose to humans. In addition to cataloguing the genotypes present using next generation sequencing technologies, researchers also enumerated the numbers of Cryptosporidium and Giardia (oo)cysts present in samples and conducted a survey of farming practices to determine if particular management practices were associated with a higher or lower prevalence of zoonotic genotypes in pre-weaned cattle and sheep.

The environmental conditions which cause blue-green algae (cyanobacteria) blooms vary according to location, the climate, and other attributes of aquatic ecosystems. This variety has made it difficult to develop one broadly applicable predictive model for cyanobacterial blooms. Water utilities monitor source waters to implement cyanobacterial risk management programmes but there are no standard protocols while limited information transfer between utilities has prevented the identification of management strategies that do or do not work. This research reviewed literature about early warning systems (Almuhtaram et al., 2021) and source control strategies, conducted a survey of 35 utilities in America and Canada (74%) and Australia (Kibuye et al., 2021) and evaluated selected control strategies. These different types of information were synthesised into decision trees within an overarching guidance document. It was concluded that a 3-tier framework to detect algal blooms which monitored biological activity, then confirmed the identification of cyanobacterial genes and associated metabolites gave sufficient early warning, while multi-barrier control strategies gave field-scale efficacy and enabled timely responses.

Cyanobacteria (blue-green algae) which float in reservoirs have been studied for decades because when they bloom, the very high cell numbers cause a problem for water treatment plant (WTP) operators, who have to remove the cells, toxins, and taste and odour compounds they produce. Benthic, bottom-living cyanobacteria which also produce toxins were recently discovered in Australian reservoirs. The problem is that benthic cyanobacteria are not included in routine monitoring practices and very little is known about them. This research provided information about the incidence of benthic cyanobacteria and the toxins they produce in various catchments; identified environmental conditions that stimulate bloom formation, and investigated naturally occurring biodegradation of taste and odour compounds. It was concluded that there is a need to monitor benthic cyanobacterial mats to ascertain the risk they pose, and to obtain additional in-situ data about more benthic species, because this will support the construction of predictive models to facilitate improved management of catchment and source waters.

Cryptosporidium, a microscopic single-cell parasite, forms an “oocyst” with a resistant outer layer analogous to an eggshell. Oocysts survive for a long time in the environment but UV in sunlight, and high temperatures that cause desiccation, kill them. If a mammal drinks water containing live oocysts, they embed in the gut wall and continue their lifecycle until eventually many more oocysts are excreted. There are 26 species of cryptosporidium but only five infect humans, and two; Cryptosporidium hominus and Cryptosporidium parvum, cause approximately 95% of all human infections. C. hominus occurs only in humans, but C. parvum is also found in cattle, sheep, and other animals. The problem is that human-infecting oocysts are excreted by animals in catchments and rain can wash live oocysts into water reservoirs. This research collated peer-reviewed published literature, and information and data collected by the water industry, then characterised the distribution of different Cryptosporidium species in Australian catchments. This led to recognition of a research need to track and predict live and dead oocyst transport during different weather events, and to model and evaluate catchment management initiatives such as excluding cattle from reservoir areas.

Pathogenic microscopic organisms in source waters pose a risk to public health if water treatment plants do not remove them. It was thought that sensitive PCR tests could be developed to inform decision-making about the most appropriate treatment processes, and to check the absence of pathogens from drinking water. This research focussed on four pathogen classes: cryptosporidium, microcystis, adenovirus and ammonia oxidising bacteria; and evaluated six DNA extraction kits. The Qiagen kit was most cost-effective for extracting DNA and Promega To-Taq polymerase was best for carrying out the PCR test on pathogens in real-world water samples. Other components of the PCR tests that were developed included test controls and DNA standards. A test for each class of pathogen was established and written as a ‘Standard Operating Protocol’ (SOP) which was then applied in different laboratories around Australia. Between-laboratory comparison of results showed the developed PCR tests to be highly reproducible and reliable. They can now be added to the existing suite of tools used to minimise risks to public health.